Vogt Lars
Institut für Evolutionsbiologie und Ökologie, Universität Bonn, An der Immenburg 1, Bonn, D-53121, Germany.
Cladistics. 2017 Oct;33(5):513-539. doi: 10.1111/cla.12179. Epub 2016 Nov 9.
The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of "characters" as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre-Darwinian comparative homology concepts and their problem of invoking non-material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer-parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.
同源性问题一直是系统生物学核心争议的根源，系统发育学中的形态特征分析步骤也是如此。基于清晰的认知框架以及将“特征”表征为识别无法直接识别实体的诊断证据单元，我讨论了系统发育同源性、发育同源性和比较同源性的本体论定义及实证识别标准，以及这三种同源性解释如何各自有助于理解同源性的整体现象。我认为系统发育同源性是需要通过比较同源性来识别的个体或历史类别。发育同源性是自然类别，最终依赖于系统发育同源性，并且也需要通过比较同源性来识别。另一方面，比较同源性是可直接识别的解剖结构类别。我讨论了达尔文之前的比较同源性概念及其调用非物质力量和涉及稳定位置参照系统先验假设的问题。基于杨的比较同源性概念，我提出了一种识别比较同源物的程序，该程序不存在这些问题并且利用了语义框架。这个形式概念框架为记录、交流和分析相似性命题提供了急需的语义透明度和计算机可解析性。它为概括个体生物体以及识别和划分解剖结构类别提供了必要的方法框架，并且为识别系统发育同源性的逻辑链提供了缺失的环节。该方法大大提高了比较研究的分析可及性，因此对形态学和比较生物学的理论和方法基础做出了重要贡献。
